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The story begins following the competition of the Holy Road soccer tournament. Tenma returns to Raimon Junior High, but finds that things have changed. The Raimon members are not soccer players. In fact, there is no soccer club at the school. Shinsuke is in a different club from Tenma. Is this a parallel world? Tenma wonders.

A future organisation called El Dorado is an organisation formed by the future world's countries to deal with important matters of world affairs, and for some reason, they've determined that soccer must be destroyed. To do so, they have assigned Alpha and his team, Protocol Omega to the mission of ridding soccer from the world.

The Inazuma Eleven GO Chrono Stone series starts after the Holy Road tournament. There are new episodes every Wednesday. Though, currently the Inazuma Eleven GO Chrono Stone anime is still not dubbed yet and has not announced an English release date yet.